\chapter{INTRO}
%This is in need of much more citation
\section{Overview}

In this document, we present research in bioinformatics ranging from the
presentation and organization of data and tools, to the utilization of
large-scale computational resources, to the implementation of novel
algorithms.  We first describe a general framework to support bioinformatics
collaborations. We then discuss principles and pitfalls in distributed
bioinformatics in the context of two example pipelines.  Finally, we present
a novel algorithm for quantifying selective pressure for rare codon clusters
in orthologs across the tree of life, leveraging principles described in the earlier chapters.

\section{Bioinformatics Web Portals}

Bioinformatics has long relied on Web Portals (ncbi, vectorbase, something else) to provide
biologists and other non-technical users with access to computing resources, tools, and data.
Here we present Biocompute, a web portal enablings large scale bioinformatics computation:
1. Interface designed to enable users
2. Distributed provisioning of resources
3. Shared capacity to bring in novel data
4. Consistent interfaces between application developers

\section{Bioinformatics Pipelines}

The proliferation of biological tools and formats has led to the common
practice of bioinformatics pipeline development.  In this chapter we discuss
the challenges involved in bioinformatics pipeline development in general, and
development of distributed pipelines in particular.  We present case studies of
pipelines in varying levels of complexity, and show the challenges involved in
scaling up using existing tools.  We document common pitfalls and workarounds
to address them.

\section{Rare Codon Analysis}
%I just wrote importantness <-- stupid
1. Background about rare codons (biology stuff)
2. Computation as a way to establish the extent of the importance of these effects 
3. We put together some of these scary pipeline things to answer this question
